I just got my '02 with the 2.7L engine (55,000 miles) back from the shop yesterday. It's been making a noise similar to the one you describe for the last 30,000 or so. It seems to start when it's about 55F outside and gets louder and takes longer to quiet down as it gets colder.
I had a lengthy conversation with the mechanic. He has 15 years of experience and after consulting with Toyota's tech line this is what he said: This is normal operation for the 2.7L. The noise is common in only the 2.7L with the one exception being certain Corollas. It is caused by different rates of thermal expansion of the materials that are used in the piston, wrist pin, and connecting rod. When it's cold out the bore in the aluminum piston and rod have more clearance than they do at higher temperatures causing the wrist pin to have excessive slop. As the engine runs, the piston heats up causing the clearance to tighten up and get rid of the slop. It is definitely not a main bearing or thrust washer because the noise fades as the engine gets warm and those noises are persistent. Because the rod swings back and forth on the wrist pin instead of rotating around it, the motion is limited and does not cause excessive wear. The noise got progressively worse when the truck was new because the wrist pin connection was wearing in. It should not change for better or worse as it ages. It also should not affect the life of the engine. While this particular engine is nosier than most, the only thing that can be done is to put in a short block, but then it would still do the same thing because it uses an identical piston, pin, and rod. Sign here and have a nice day.
I initially thought valve train noise also, because the rate at which I hear the noise seems to be about half of what the engine is turning. I asked him about this and he said definitely not at which point he launched into a solo discussion about main bearing and thrust washer noise. I also hear only one cylinder doing it instead of all of them, which leads me to think that I got a piston, pin, rod combo whose tolerances stacked up in the wrong direction. In any case I question whether this is a defect or not. Just because it’s normal doesn’t mean it’s right.